DE analysis
gn <- as.character(ls_preprocessed$rna_all$Feature[which(ls_preprocessed$rna_all$Feature_gene_name =='BAP1')])
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=TRUE,
pDataBased=FALSE,
NewCondition=FALSE,
cond_nm= gn,
reference = 'low',
correct_gender=TRUE,
extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1192 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done
DE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- gn
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='BAP1', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)
vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
| 6.395729e+01 |
3.905607 |
0.4079837 |
4.461556 |
0.0000081 |
0.0001766 |
ENSG00000263076.1 |
RPS9 |
FC_P |
RPS9 |
3.905607 |
0.0000081 |
| 7.434226e+01 |
-3.602810 |
0.3643107 |
-3.743773 |
0.0001813 |
0.0019834 |
ENSG00000094755.12 |
GABRP |
FC_P |
GABRP |
-3.602810 |
0.0001813 |
| 3.568936e+02 |
-3.477134 |
0.4061124 |
-8.802162 |
0.0000000 |
0.0000000 |
ENSG00000139144.5 |
PIK3C2G |
FC_P |
PIK3C2G |
-3.477134 |
0.0000000 |
| 1.364547e+02 |
-3.181504 |
0.3879255 |
-6.556765 |
0.0000000 |
0.0000000 |
ENSG00000109511.6 |
ANXA10 |
FC_P |
ANXA10 |
-3.181504 |
0.0000000 |
| 5.915634e+00 |
-3.075488 |
0.4096229 |
-3.759272 |
0.0001704 |
0.0018910 |
ENSG00000180251.4 |
SLC9A4 |
FC_P |
SLC9A4 |
-3.075488 |
0.0001704 |
| 1.680560e+02 |
-2.851171 |
0.4087265 |
-7.344544 |
0.0000000 |
0.0000000 |
ENSG00000198758.6 |
EPS8L3 |
FC_P |
EPS8L3 |
-2.851171 |
0.0000000 |
| 3.089430e+01 |
-2.779230 |
0.4053354 |
-6.896032 |
0.0000000 |
0.0000000 |
ENSG00000139151.10 |
PLCZ1 |
FC_P |
PLCZ1 |
-2.779230 |
0.0000000 |
| 8.698395e+00 |
-2.763408 |
0.4376922 |
-4.052550 |
0.0000507 |
0.0007386 |
ENSG00000213759.4 |
UGT2B11 |
FC_P |
UGT2B11 |
-2.763408 |
0.0000507 |
| 1.700950e+01 |
-2.663663 |
0.4038956 |
-3.577265 |
0.0003472 |
0.0032632 |
ENSG00000179674.2 |
ARL14 |
FC_P |
ARL14 |
-2.663663 |
0.0003472 |
| 1.565666e+01 |
-2.659716 |
0.4341733 |
-6.456752 |
0.0000000 |
0.0000000 |
ENSG00000255960.1 |
RP11-459D22.1 |
FC_P |
RP11.459D22.1 |
-2.659716 |
0.0000000 |
| 8.598807e+00 |
-2.537779 |
0.3983237 |
-6.222362 |
0.0000000 |
0.0000001 |
ENSG00000206918.1 |
RNU6-1181P |
FC_P |
RNU6.1181P |
-2.537779 |
0.0000000 |
| 1.703118e+01 |
-2.437372 |
0.3881446 |
-6.224429 |
0.0000000 |
0.0000001 |
ENSG00000264727.1 |
RP11-680C21.1 |
FC_P |
RP11.680C21.1 |
-2.437372 |
0.0000000 |
| 5.309453e+01 |
-2.432980 |
0.3995047 |
-6.091562 |
0.0000000 |
0.0000001 |
ENSG00000255745.1 |
RP11-625L16.1 |
FC_P |
RP11.625L16.1 |
-2.432980 |
0.0000000 |
| 4.953813e+01 |
-2.421761 |
0.4028772 |
-6.188719 |
0.0000000 |
0.0000001 |
ENSG00000231738.6 |
TSPAN19 |
FC_P |
TSPAN19 |
-2.421761 |
0.0000000 |
| 5.463126e+01 |
-2.361731 |
0.4178989 |
-6.202472 |
0.0000000 |
0.0000001 |
ENSG00000180861.5 |
C12orf36 |
FC_P |
C12orf36 |
-2.361731 |
0.0000000 |
| 1.050103e+01 |
-2.256090 |
0.4354248 |
-5.374849 |
0.0000001 |
0.0000042 |
ENSG00000272609.1 |
RP11-461M2.2 |
FC_P |
RP11.461M2.2 |
-2.256090 |
0.0000001 |
| 1.777785e+03 |
-2.246058 |
0.3260558 |
-6.891107 |
0.0000000 |
0.0000000 |
ENSG00000106258.9 |
CYP3A5 |
FC_P |
CYP3A5 |
-2.246058 |
0.0000000 |
| 1.145266e+01 |
-2.221131 |
0.4247219 |
-3.961601 |
0.0000744 |
0.0009940 |
ENSG00000096006.7 |
CRISP3 |
FC_P |
CRISP3 |
-2.221131 |
0.0000744 |
| 3.845727e+02 |
2.216497 |
0.3960091 |
5.543714 |
0.0000000 |
0.0000020 |
ENSG00000178343.4 |
SHISA3 |
FC_P |
SHISA3 |
2.216497 |
0.0000000 |
| 4.740936e+01 |
-2.211727 |
0.3842247 |
-5.745174 |
0.0000000 |
0.0000008 |
ENSG00000185860.9 |
C1orf110 |
FC_P |
C1orf110 |
-2.211727 |
0.0000000 |
| 2.762336e+00 |
-2.189313 |
0.4089859 |
-5.199607 |
0.0000002 |
0.0000092 |
ENSG00000234497.1 |
RP4-612J11.1 |
FC_P |
RP4.612J11.1 |
-2.189313 |
0.0000002 |
| 9.540603e+00 |
-2.167287 |
0.4045146 |
-5.321060 |
0.0000001 |
0.0000054 |
ENSG00000265374.1 |
RP11-57J16.1 |
FC_P |
RP11.57J16.1 |
-2.167287 |
0.0000001 |
| 6.927466e+00 |
-2.161285 |
0.3843989 |
-5.528617 |
0.0000000 |
0.0000021 |
ENSG00000224493.1 |
RP11-87O11.1 |
FC_P |
RP11.87O11.1 |
-2.161285 |
0.0000000 |
| 2.699128e+00 |
-2.150376 |
0.3770574 |
-5.482018 |
0.0000000 |
0.0000026 |
ENSG00000201392.1 |
RNU6-1078P |
FC_P |
RNU6.1078P |
-2.150376 |
0.0000000 |
| 2.632303e+00 |
-2.136931 |
0.3878510 |
-5.353384 |
0.0000001 |
0.0000047 |
ENSG00000231080.1 |
RP11-342H21.2 |
FC_P |
RP11.342H21.2 |
-2.136931 |
0.0000001 |
| 1.046986e+02 |
-2.136067 |
0.4013775 |
-5.870197 |
0.0000000 |
0.0000004 |
ENSG00000198643.2 |
FAM3D |
FC_P |
FAM3D |
-2.136067 |
0.0000000 |
| 8.313274e+01 |
-2.126918 |
0.3681818 |
-5.774856 |
0.0000000 |
0.0000007 |
ENSG00000118492.12 |
ADGB |
FC_P |
ADGB |
-2.126918 |
0.0000000 |
| 6.619559e+00 |
-2.122946 |
0.3769792 |
-5.495207 |
0.0000000 |
0.0000024 |
ENSG00000254878.1 |
CTD-3096P4.1 |
FC_P |
CTD.3096P4.1 |
-2.122946 |
0.0000000 |
| 2.223428e+02 |
-2.121234 |
0.4131340 |
-5.221776 |
0.0000002 |
0.0000084 |
ENSG00000166959.3 |
MS4A8 |
FC_P |
MS4A8 |
-2.121234 |
0.0000002 |
| 9.753472e+00 |
-2.119295 |
0.4378337 |
-5.141038 |
0.0000003 |
0.0000118 |
ENSG00000255892.1 |
RP11-459D22.2 |
FC_P |
RP11.459D22.2 |
-2.119295 |
0.0000003 |
| 3.292266e+00 |
-2.117288 |
0.4184216 |
-4.734363 |
0.0000022 |
0.0000632 |
ENSG00000253622.1 |
RP11-654G14.1 |
FC_P |
RP11.654G14.1 |
-2.117288 |
0.0000022 |
| 3.057300e+01 |
-2.102215 |
0.3593455 |
-5.852412 |
0.0000000 |
0.0000004 |
ENSG00000183644.9 |
C11orf88 |
FC_P |
C11orf88 |
-2.102215 |
0.0000000 |
| 3.057907e+00 |
-2.099597 |
0.4040851 |
-5.079014 |
0.0000004 |
0.0000154 |
ENSG00000221436.1 |
MIR548F3 |
FC_P |
MIR548F3 |
-2.099597 |
0.0000004 |
| 1.887166e+01 |
-2.092479 |
0.3489431 |
-5.970496 |
0.0000000 |
0.0000003 |
ENSG00000124564.13 |
SLC17A3 |
FC_P |
SLC17A3 |
-2.092479 |
0.0000000 |
| 3.284765e+01 |
-2.069994 |
0.3722642 |
-5.587361 |
0.0000000 |
0.0000016 |
ENSG00000152936.6 |
IFLTD1 |
FC_P |
IFLTD1 |
-2.069994 |
0.0000000 |
| 5.937833e+00 |
-2.062259 |
0.4092754 |
-5.138920 |
0.0000003 |
0.0000119 |
ENSG00000269916.1 |
RP11-193M21.1 |
FC_P |
RP11.193M21.1 |
-2.062259 |
0.0000003 |
| 1.454277e+02 |
-2.043549 |
0.3876956 |
-5.264933 |
0.0000001 |
0.0000069 |
ENSG00000015520.10 |
NPC1L1 |
FC_P |
NPC1L1 |
-2.043549 |
0.0000001 |
| 3.642398e+02 |
-2.040786 |
0.4052670 |
-5.161997 |
0.0000002 |
0.0000108 |
ENSG00000171747.4 |
LGALS4 |
FC_P |
LGALS4 |
-2.040786 |
0.0000002 |
| 4.116681e+00 |
-2.023286 |
0.4150570 |
-4.806811 |
0.0000015 |
0.0000468 |
ENSG00000236164.1 |
RP11-268F1.3 |
FC_P |
RP11.268F1.3 |
-2.023286 |
0.0000015 |
| 3.250756e+01 |
-2.018262 |
0.2342670 |
-4.315903 |
0.0000159 |
0.0002980 |
ENSG00000137860.7 |
SLC28A2 |
FC_P |
SLC28A2 |
-2.018262 |
0.0000159 |
| 1.147143e+01 |
-2.015023 |
0.4319118 |
-4.890826 |
0.0000010 |
0.0000333 |
ENSG00000176571.7 |
CNBD1 |
FC_P |
CNBD1 |
-2.015023 |
0.0000010 |
| 3.843674e+02 |
-2.008995 |
0.3289891 |
-6.107607 |
0.0000000 |
0.0000001 |
ENSG00000174844.10 |
DNAH12 |
FC_P |
DNAH12 |
-2.008995 |
0.0000000 |
| 5.518288e+01 |
-1.994169 |
0.3984189 |
-4.943332 |
0.0000008 |
0.0000269 |
ENSG00000113303.7 |
BTNL8 |
FC_P |
BTNL8 |
-1.994169 |
0.0000008 |
| 3.534691e+01 |
-1.972888 |
0.4013390 |
-4.933334 |
0.0000008 |
0.0000281 |
ENSG00000224259.1 |
RP11-48O20.4 |
FC_P |
RP11.48O20.4 |
-1.972888 |
0.0000008 |
| 1.913498e+02 |
-1.972476 |
0.3265393 |
-6.078994 |
0.0000000 |
0.0000001 |
ENSG00000179813.2 |
FAM216B |
FC_P |
FAM216B |
-1.972476 |
0.0000000 |
| 2.915134e+00 |
-1.967581 |
0.4173450 |
-4.620100 |
0.0000038 |
0.0000986 |
ENSG00000250961.1 |
CTD-2023N9.1 |
FC_P |
CTD.2023N9.1 |
-1.967581 |
0.0000038 |
| 6.459530e+00 |
-1.955358 |
0.4266388 |
-4.812671 |
0.0000015 |
0.0000456 |
ENSG00000109205.12 |
ODAM |
FC_P |
ODAM |
-1.955358 |
0.0000015 |
| 1.060466e+02 |
-1.950554 |
0.4303060 |
-4.570237 |
0.0000049 |
0.0001187 |
ENSG00000101076.12 |
HNF4A |
FC_P |
HNF4A |
-1.950554 |
0.0000049 |
| 4.903937e+01 |
-1.941008 |
0.3795627 |
-4.909471 |
0.0000009 |
0.0000310 |
ENSG00000259871.1 |
CTA-363E6.1 |
FC_P |
CTA.363E6.1 |
-1.941008 |
0.0000009 |
| 1.654734e+01 |
-1.927166 |
0.3398336 |
-5.655685 |
0.0000000 |
0.0000012 |
ENSG00000152595.12 |
MEPE |
FC_P |
MEPE |
-1.927166 |
0.0000000 |
| 4.787161e+01 |
1.922242 |
0.3860571 |
5.020664 |
0.0000005 |
0.0000194 |
ENSG00000156959.7 |
LHFPL4 |
FC_P |
LHFPL4 |
1.922242 |
0.0000005 |
| 1.619878e+01 |
-1.914762 |
0.3512283 |
-5.458547 |
0.0000000 |
0.0000029 |
ENSG00000178125.10 |
PPP1R42 |
FC_P |
PPP1R42 |
-1.914762 |
0.0000000 |
| 1.402639e+01 |
-1.914343 |
0.3519080 |
-5.434830 |
0.0000001 |
0.0000032 |
ENSG00000111404.2 |
RERGL |
FC_P |
RERGL |
-1.914343 |
0.0000001 |
| 4.324700e+00 |
-1.908944 |
0.4002577 |
-4.751821 |
0.0000020 |
0.0000588 |
ENSG00000259833.1 |
RP11-23E19.1 |
FC_P |
RP11.23E19.1 |
-1.908944 |
0.0000020 |
| 1.723749e+03 |
-1.908686 |
0.4054201 |
-4.736682 |
0.0000022 |
0.0000625 |
ENSG00000125999.6 |
BPIFB1 |
FC_P |
BPIFB1 |
-1.908686 |
0.0000022 |
| 1.394267e+01 |
-1.901706 |
0.4356505 |
-4.593225 |
0.0000044 |
0.0001090 |
ENSG00000257454.1 |
CTD-2021H9.2 |
FC_P |
CTD.2021H9.2 |
-1.901706 |
0.0000044 |
| 1.399229e+01 |
-1.898384 |
0.3520687 |
-5.372038 |
0.0000001 |
0.0000043 |
ENSG00000231204.1 |
AC011752.1 |
FC_P |
AC011752.1 |
-1.898384 |
0.0000001 |
| 6.104181e+00 |
-1.896846 |
0.3201263 |
-5.924827 |
0.0000000 |
0.0000003 |
ENSG00000265042.1 |
AL137800.1 |
FC_P |
AL137800.1 |
-1.896846 |
0.0000000 |
| 6.337819e+00 |
-1.885726 |
0.4142377 |
-4.584775 |
0.0000045 |
0.0001125 |
ENSG00000230739.1 |
RP11-331H2.4 |
FC_P |
RP11.331H2.4 |
-1.885726 |
0.0000045 |
| 5.324843e+01 |
-1.874704 |
0.3643601 |
-5.180296 |
0.0000002 |
0.0000100 |
ENSG00000231980.1 |
AC011899.10 |
FC_P |
AC011899.10 |
-1.874704 |
0.0000002 |
| 1.711681e+02 |
-1.864090 |
0.3677366 |
-5.088596 |
0.0000004 |
0.0000147 |
ENSG00000169064.8 |
ZBBX |
FC_P |
ZBBX |
-1.864090 |
0.0000004 |
| 4.820517e+01 |
-1.863829 |
0.4361304 |
-4.991890 |
0.0000006 |
0.0000221 |
ENSG00000205922.4 |
ONECUT3 |
FC_P |
ONECUT3 |
-1.863829 |
0.0000006 |
| 1.055252e+03 |
-1.862965 |
0.3902522 |
-4.904527 |
0.0000009 |
0.0000315 |
ENSG00000127324.4 |
TSPAN8 |
FC_P |
TSPAN8 |
-1.862965 |
0.0000009 |
| 1.017633e+01 |
-1.853212 |
0.3935168 |
-4.807918 |
0.0000015 |
0.0000467 |
ENSG00000236460.1 |
SNX2P2 |
FC_P |
SNX2P2 |
-1.853212 |
0.0000015 |
| 1.260226e+02 |
-1.845505 |
0.3475012 |
-5.323896 |
0.0000001 |
0.0000053 |
ENSG00000170324.15 |
FRMPD2 |
FC_P |
FRMPD2 |
-1.845505 |
0.0000001 |
| 1.157815e+01 |
-1.834585 |
0.4364329 |
-4.584523 |
0.0000046 |
0.0001126 |
ENSG00000229005.2 |
RP5-881L22.4 |
FC_P |
RP5.881L22.4 |
-1.834585 |
0.0000046 |
| 2.377084e+02 |
-1.828788 |
0.3705012 |
-4.817670 |
0.0000015 |
0.0000446 |
ENSG00000254608.1 |
RP11-56A10.1 |
FC_P |
RP11.56A10.1 |
-1.828788 |
0.0000015 |
| 4.557000e+00 |
-1.826705 |
0.4054238 |
-4.466473 |
0.0000080 |
0.0001739 |
ENSG00000232462.1 |
RP11-13E1.5 |
FC_P |
RP11.13E1.5 |
-1.826705 |
0.0000080 |
| 2.690914e+01 |
-1.822595 |
0.4110993 |
-4.486034 |
0.0000073 |
0.0001611 |
ENSG00000186329.5 |
TMEM212 |
FC_P |
TMEM212 |
-1.822595 |
0.0000073 |
| 1.006642e+01 |
1.815546 |
0.4017259 |
4.335830 |
0.0000145 |
0.0002796 |
ENSG00000227656.3 |
RPL3P2 |
FC_P |
RPL3P2 |
1.815546 |
0.0000145 |
| 1.067424e+02 |
-1.808680 |
0.3697544 |
-5.089734 |
0.0000004 |
0.0000147 |
ENSG00000115616.2 |
SLC9A2 |
FC_P |
SLC9A2 |
-1.808680 |
0.0000004 |
| 2.800994e+01 |
-1.805767 |
0.3778649 |
-4.796064 |
0.0000016 |
0.0000489 |
ENSG00000152611.7 |
CAPSL |
FC_P |
CAPSL |
-1.805767 |
0.0000016 |
| 7.954587e+01 |
-1.804249 |
0.4028713 |
-4.263718 |
0.0000201 |
0.0003557 |
ENSG00000144852.12 |
NR1I2 |
FC_P |
NR1I2 |
-1.804249 |
0.0000201 |
| 3.353307e+01 |
-1.803266 |
0.3597823 |
-5.000164 |
0.0000006 |
0.0000212 |
ENSG00000231606.1 |
RP11-344F13.1 |
FC_P |
RP11.344F13.1 |
-1.803266 |
0.0000006 |
| 6.697073e+00 |
-1.803135 |
0.4347802 |
-4.650053 |
0.0000033 |
0.0000883 |
ENSG00000170788.9 |
DYDC1 |
FC_P |
DYDC1 |
-1.803135 |
0.0000033 |
| 3.387660e+02 |
-1.794276 |
0.4286749 |
-4.220637 |
0.0000244 |
0.0004161 |
ENSG00000183778.13 |
B3GALT5 |
FC_P |
B3GALT5 |
-1.794276 |
0.0000244 |
| 3.627475e+01 |
-1.792554 |
0.3756921 |
-4.752823 |
0.0000020 |
0.0000586 |
ENSG00000197826.7 |
C4orf22 |
FC_P |
C4orf22 |
-1.792554 |
0.0000020 |
| 2.899941e+01 |
-1.788535 |
0.4356225 |
-4.513469 |
0.0000064 |
0.0001457 |
ENSG00000233377.1 |
MTND4P20 |
FC_P |
MTND4P20 |
-1.788535 |
0.0000064 |
| 4.812892e+00 |
-1.787645 |
0.3699238 |
-4.844228 |
0.0000013 |
0.0000402 |
ENSG00000272508.1 |
RP11-96C23.14 |
FC_P |
RP11.96C23.14 |
-1.787645 |
0.0000013 |
| 2.953442e+01 |
-1.787242 |
0.4050641 |
-4.748168 |
0.0000021 |
0.0000596 |
ENSG00000153822.9 |
KCNJ16 |
FC_P |
KCNJ16 |
-1.787242 |
0.0000021 |
| 2.071817e+02 |
-1.786619 |
0.3557032 |
-5.359911 |
0.0000001 |
0.0000046 |
ENSG00000173597.4 |
SULT1B1 |
FC_P |
SULT1B1 |
-1.786619 |
0.0000001 |
| 1.214391e+01 |
-1.777301 |
0.2873209 |
-6.154611 |
0.0000000 |
0.0000001 |
ENSG00000212259.1 |
RNU6-308P |
FC_P |
RNU6.308P |
-1.777301 |
0.0000000 |
| 2.772308e+00 |
-1.765928 |
0.4335961 |
-4.246971 |
0.0000217 |
0.0003783 |
ENSG00000199798.1 |
SNORD114-5 |
FC_P |
SNORD114.5 |
-1.765928 |
0.0000217 |
| 1.376221e+01 |
-1.760880 |
0.3927977 |
-4.968263 |
0.0000007 |
0.0000242 |
ENSG00000212384.1 |
SNORD113-2 |
FC_P |
SNORD113.2 |
-1.760880 |
0.0000007 |
| 1.186392e+03 |
1.758429 |
0.3258986 |
5.672778 |
0.0000000 |
0.0000011 |
ENSG00000272060.1 |
RNA18S5 |
FC_P |
RNA18S5 |
1.758429 |
0.0000000 |
| 7.782392e+00 |
-1.742614 |
0.3480489 |
-4.976612 |
0.0000006 |
0.0000233 |
ENSG00000252145.1 |
RNU6-1225P |
FC_P |
RNU6.1225P |
-1.742614 |
0.0000006 |
| 5.614511e+00 |
-1.741985 |
0.3239441 |
-5.322892 |
0.0000001 |
0.0000053 |
ENSG00000267316.1 |
RP11-879F14.3 |
FC_P |
RP11.879F14.3 |
-1.741985 |
0.0000001 |
| 5.588912e+01 |
-1.736783 |
0.3761547 |
-4.626557 |
0.0000037 |
0.0000961 |
ENSG00000176034.8 |
CHDC2 |
FC_P |
CHDC2 |
-1.736783 |
0.0000037 |
| 3.671876e+01 |
-1.735247 |
0.3888346 |
-4.132938 |
0.0000358 |
0.0005608 |
ENSG00000179008.4 |
C14orf39 |
FC_P |
C14orf39 |
-1.735247 |
0.0000358 |
| 2.799997e+01 |
-1.733726 |
0.4264337 |
-4.232982 |
0.0000231 |
0.0003975 |
ENSG00000258053.1 |
CTD-2021H9.3 |
FC_P |
CTD.2021H9.3 |
-1.733726 |
0.0000231 |
| 2.476614e+01 |
-1.732557 |
0.3719044 |
-4.806639 |
0.0000015 |
0.0000468 |
ENSG00000116785.9 |
CFHR3 |
FC_P |
CFHR3 |
-1.732557 |
0.0000015 |
| 6.709973e+00 |
-1.730895 |
0.3949433 |
-4.469892 |
0.0000078 |
0.0001717 |
ENSG00000231688.1 |
RPL21P43 |
FC_P |
RPL21P43 |
-1.730895 |
0.0000078 |
| 4.280093e+00 |
-1.725939 |
0.4206881 |
-4.133070 |
0.0000358 |
0.0005607 |
ENSG00000272474.1 |
SNORD113-5 |
FC_P |
SNORD113.5 |
-1.725939 |
0.0000358 |
| 2.252063e+02 |
1.725812 |
0.4345496 |
3.674346 |
0.0002385 |
0.0024535 |
ENSG00000184937.8 |
WT1 |
FC_P |
WT1 |
1.725812 |
0.0002385 |
| 8.437506e+01 |
-1.725060 |
0.3861698 |
-4.336275 |
0.0000145 |
0.0002793 |
ENSG00000261210.1 |
CLEC19A |
FC_P |
CLEC19A |
-1.725060 |
0.0000145 |
| 2.357202e+01 |
-1.722434 |
0.3038579 |
-5.690980 |
0.0000000 |
0.0000010 |
ENSG00000201852.1 |
RNU6-702P |
FC_P |
RNU6.702P |
-1.722434 |
0.0000000 |
| 9.747567e+01 |
-1.721685 |
0.3738661 |
-4.475010 |
0.0000076 |
0.0001686 |
ENSG00000188477.8 |
AC003003.5 |
FC_P |
AC003003.5 |
-1.721685 |
0.0000076 |
| 6.351681e+00 |
-1.720670 |
0.4069225 |
-4.285843 |
0.0000182 |
0.0003318 |
ENSG00000213579.3 |
RP4-595K12.1 |
FC_P |
RP4.595K12.1 |
-1.720670 |
0.0000182 |
| 9.808668e+00 |
1.718650 |
0.3632088 |
4.523860 |
0.0000061 |
0.0001405 |
ENSG00000238531.1 |
SNORD105B |
FC_P |
SNORD105B |
1.718650 |
0.0000061 |
| 2.341197e+00 |
-1.715618 |
0.4330651 |
-3.833136 |
0.0001265 |
0.0014934 |
ENSG00000252266.1 |
Y_RNA |
FC_P |
Y_RNA |
-1.715618 |
0.0001265 |
| 4.709991e+00 |
-1.711718 |
0.3470465 |
-4.896369 |
0.0000010 |
0.0000327 |
ENSG00000207769.1 |
MIR586 |
FC_P |
MIR586 |
-1.711718 |
0.0000010 |
| 8.961454e+00 |
-1.705116 |
0.2895962 |
-5.930252 |
0.0000000 |
0.0000003 |
ENSG00000199551.1 |
RNU6-545P |
FC_P |
RNU6.545P |
-1.705116 |
0.0000000 |
| 6.418227e+00 |
-1.705062 |
0.4094651 |
-4.149423 |
0.0000333 |
0.0005303 |
ENSG00000225738.2 |
NRG3-AS1 |
FC_P |
NRG3.AS1 |
-1.705062 |
0.0000333 |
| 4.311073e+00 |
-1.702169 |
0.4272429 |
-3.993381 |
0.0000651 |
0.0008962 |
ENSG00000253500.1 |
AF121898.3 |
FC_P |
AF121898.3 |
-1.702169 |
0.0000651 |
| 1.395055e+02 |
-1.698388 |
0.3846098 |
-4.431054 |
0.0000094 |
0.0001989 |
ENSG00000178965.9 |
C1orf173 |
FC_P |
C1orf173 |
-1.698388 |
0.0000094 |
| 1.857221e+02 |
-1.697836 |
0.4355724 |
-3.737769 |
0.0001857 |
0.0020190 |
ENSG00000006611.11 |
USH1C |
FC_P |
USH1C |
-1.697836 |
0.0001857 |
| 2.710706e+01 |
-1.695581 |
0.3826837 |
-4.350390 |
0.0000136 |
0.0002666 |
ENSG00000253496.2 |
RP11-13N12.1 |
FC_P |
RP11.13N12.1 |
-1.695581 |
0.0000136 |
| 2.727041e+01 |
1.694221 |
0.4377222 |
4.317120 |
0.0000158 |
0.0002968 |
ENSG00000229544.6 |
NKX1-2 |
FC_P |
NKX1.2 |
1.694221 |
0.0000158 |
| 8.485052e+02 |
1.687851 |
0.2883636 |
5.803415 |
0.0000000 |
0.0000006 |
ENSG00000266219.1 |
AL592188.8 |
FC_P |
AL592188.8 |
1.687851 |
0.0000000 |
| 1.470123e+02 |
1.687124 |
0.3085721 |
5.392887 |
0.0000001 |
0.0000039 |
ENSG00000252139.1 |
SCARNA18 |
FC_P |
SCARNA18 |
1.687124 |
0.0000001 |
| 9.626820e+00 |
-1.686557 |
0.3331058 |
-5.200573 |
0.0000002 |
0.0000091 |
ENSG00000253576.1 |
GS1-5L10.1 |
FC_P |
GS1.5L10.1 |
-1.686557 |
0.0000002 |
| 2.313546e+01 |
-1.685894 |
0.2733041 |
-6.253703 |
0.0000000 |
0.0000001 |
ENSG00000258026.1 |
RP11-543H12.1 |
FC_P |
RP11.543H12.1 |
-1.685894 |
0.0000000 |
| 6.219826e+00 |
-1.683636 |
0.4240010 |
-3.965518 |
0.0000732 |
0.0009812 |
ENSG00000255993.1 |
PSMC1P9 |
FC_P |
PSMC1P9 |
-1.683636 |
0.0000732 |
| 1.988843e+01 |
-1.678026 |
0.2695354 |
-6.221283 |
0.0000000 |
0.0000001 |
ENSG00000234523.1 |
NDUFB1P2 |
FC_P |
NDUFB1P2 |
-1.678026 |
0.0000000 |
| 5.995542e+01 |
-1.672144 |
0.3507616 |
-4.784304 |
0.0000017 |
0.0000514 |
ENSG00000170703.11 |
TTLL6 |
FC_P |
TTLL6 |
-1.672144 |
0.0000017 |
| 2.595302e+01 |
-1.670899 |
0.3929936 |
-4.280856 |
0.0000186 |
0.0003374 |
ENSG00000133115.7 |
STOML3 |
FC_P |
STOML3 |
-1.670899 |
0.0000186 |
| 9.164636e+00 |
-1.667301 |
0.2625477 |
-6.319647 |
0.0000000 |
0.0000000 |
ENSG00000216205.1 |
AC036178.1 |
FC_P |
AC036178.1 |
-1.667301 |
0.0000000 |
| 2.574318e+01 |
-1.663684 |
0.3530013 |
-3.392622 |
0.0006923 |
0.0055673 |
ENSG00000122012.9 |
SV2C |
FC_P |
SV2C |
-1.663684 |
0.0006923 |
| 9.447488e+02 |
-1.658676 |
0.3765336 |
-4.116985 |
0.0000384 |
0.0005914 |
ENSG00000104237.6 |
RP1 |
FC_P |
RP1 |
-1.658676 |
0.0000384 |
| 7.777534e+00 |
-1.657092 |
0.3628047 |
-4.537816 |
0.0000057 |
0.0001341 |
ENSG00000223015.1 |
RNU6-1135P |
FC_P |
RNU6.1135P |
-1.657092 |
0.0000057 |
| 1.077423e+02 |
-1.657082 |
0.2425042 |
-6.846682 |
0.0000000 |
0.0000000 |
ENSG00000117501.10 |
MROH9 |
FC_P |
MROH9 |
-1.657082 |
0.0000000 |
| 2.692793e+01 |
1.655353 |
0.3899967 |
3.785196 |
0.0001536 |
0.0017410 |
ENSG00000210077.1 |
MT-TV |
FC_P |
MT.TV |
1.655353 |
0.0001536 |
| 4.702193e+00 |
1.653824 |
0.4018464 |
4.138235 |
0.0000350 |
0.0005508 |
ENSG00000229172.1 |
AC073065.3 |
FC_P |
AC073065.3 |
1.653824 |
0.0000350 |
| 5.030414e+00 |
-1.652382 |
0.3793573 |
-4.481994 |
0.0000074 |
0.0001638 |
ENSG00000221249.1 |
AC004980.1 |
FC_P |
AC004980.1 |
-1.652382 |
0.0000074 |
| 2.152592e+01 |
-1.651480 |
0.3030535 |
-5.625535 |
0.0000000 |
0.0000013 |
ENSG00000271730.1 |
RP11-787I22.3 |
FC_P |
RP11.787I22.3 |
-1.651480 |
0.0000000 |
| 2.921686e+01 |
1.649626 |
0.3594210 |
4.578599 |
0.0000047 |
0.0001151 |
ENSG00000115138.6 |
POMC |
FC_P |
POMC |
1.649626 |
0.0000047 |
| 6.892794e+00 |
-1.647152 |
0.4081034 |
-4.084261 |
0.0000442 |
0.0006606 |
ENSG00000256717.1 |
AP000797.3 |
FC_P |
AP000797.3 |
-1.647152 |
0.0000442 |
| 1.502092e+00 |
-1.646279 |
0.4321745 |
-3.669846 |
0.0002427 |
0.0024882 |
ENSG00000238770.1 |
snoU13 |
FC_P |
snoU13 |
-1.646279 |
0.0002427 |
| 6.298731e+00 |
-1.644446 |
0.3574308 |
-4.531219 |
0.0000059 |
0.0001366 |
ENSG00000264470.1 |
MIR4794 |
FC_P |
MIR4794 |
-1.644446 |
0.0000059 |
| 7.878457e+01 |
-1.643886 |
0.3513834 |
-4.947666 |
0.0000008 |
0.0000264 |
ENSG00000200389.1 |
RNU6-509P |
FC_P |
RNU6.509P |
-1.643886 |
0.0000008 |
| 5.188219e+00 |
-1.639926 |
0.4230211 |
-4.085930 |
0.0000439 |
0.0006566 |
ENSG00000240666.1 |
MME-AS1 |
FC_P |
MME.AS1 |
-1.639926 |
0.0000439 |
| 8.337960e+01 |
-1.638588 |
0.3654787 |
-4.487690 |
0.0000072 |
0.0001602 |
ENSG00000165164.8 |
CXorf22 |
FC_P |
CXorf22 |
-1.638588 |
0.0000072 |
| 1.383801e+01 |
1.633614 |
0.4025336 |
3.744339 |
0.0001809 |
0.0019801 |
ENSG00000237222.3 |
AC090505.6 |
FC_P |
AC090505.6 |
1.633614 |
0.0001809 |
| 8.191233e+01 |
-1.632666 |
0.3806674 |
-4.093422 |
0.0000425 |
0.0006403 |
ENSG00000223561.2 |
AC003090.1 |
FC_P |
AC003090.1 |
-1.632666 |
0.0000425 |
| 9.166382e+00 |
-1.630897 |
0.3795985 |
-4.275920 |
0.0000190 |
0.0003429 |
ENSG00000080572.8 |
PIH1D3 |
FC_P |
PIH1D3 |
-1.630897 |
0.0000190 |
| 2.196298e+01 |
-1.627392 |
0.3102061 |
-5.252599 |
0.0000001 |
0.0000073 |
ENSG00000257467.1 |
RP11-121G22.3 |
FC_P |
RP11.121G22.3 |
-1.627392 |
0.0000001 |
| 5.341559e+00 |
-1.625179 |
0.3598192 |
-4.437266 |
0.0000091 |
0.0001938 |
ENSG00000246016.2 |
RP11-1C1.7 |
FC_P |
RP11.1C1.7 |
-1.625179 |
0.0000091 |
| 1.228739e+01 |
-1.624600 |
0.3252000 |
-5.023798 |
0.0000005 |
0.0000192 |
ENSG00000239119.1 |
RNU7-119P |
FC_P |
RNU7.119P |
-1.624600 |
0.0000005 |
| 1.342024e+01 |
-1.622414 |
0.2778539 |
-5.868876 |
0.0000000 |
0.0000004 |
ENSG00000206700.1 |
RNU6-723P |
FC_P |
RNU6.723P |
-1.622414 |
0.0000000 |
| 9.077770e+00 |
-1.618259 |
0.2876106 |
-5.678807 |
0.0000000 |
0.0000011 |
ENSG00000199790.1 |
RNU6-836P |
FC_P |
RNU6.836P |
-1.618259 |
0.0000000 |
| 9.915807e+00 |
-1.617854 |
0.4114030 |
-4.034653 |
0.0000547 |
0.0007835 |
ENSG00000255666.1 |
RP11-867G2.6 |
FC_P |
RP11.867G2.6 |
-1.617854 |
0.0000547 |
| 1.198596e+01 |
-1.617547 |
0.3742146 |
-4.341998 |
0.0000141 |
0.0002737 |
ENSG00000227274.1 |
AC005358.3 |
FC_P |
AC005358.3 |
-1.617547 |
0.0000141 |
| 3.609974e+00 |
-1.616071 |
0.3590620 |
-4.570040 |
0.0000049 |
0.0001187 |
ENSG00000201984.1 |
Y_RNA |
FC_P |
Y_RNA.1 |
-1.616071 |
0.0000049 |
| 1.228715e+01 |
1.614902 |
0.3584603 |
4.449898 |
0.0000086 |
0.0001845 |
ENSG00000146090.11 |
RASGEF1C |
FC_P |
RASGEF1C |
1.614902 |
0.0000086 |
| 3.500915e+01 |
-1.613115 |
0.3701629 |
-4.358204 |
0.0000131 |
0.0002582 |
ENSG00000148584.10 |
A1CF |
FC_P |
A1CF |
-1.613115 |
0.0000131 |
| 1.194109e+05 |
1.612413 |
0.2696172 |
5.942833 |
0.0000000 |
0.0000003 |
ENSG00000264462.1 |
MIR3648 |
FC_P |
MIR3648 |
1.612413 |
0.0000000 |
| 9.589887e+00 |
-1.610169 |
0.4021951 |
-4.015403 |
0.0000593 |
0.0008330 |
ENSG00000188729.2 |
OSTN |
FC_P |
OSTN |
-1.610169 |
0.0000593 |
| 1.338768e+00 |
-1.609817 |
0.4331838 |
-3.738311 |
0.0001853 |
0.0020170 |
ENSG00000235858.1 |
RP11-36D19.8 |
FC_P |
RP11.36D19.8 |
-1.609817 |
0.0001853 |
| 1.176743e+03 |
1.607707 |
0.2946436 |
5.461828 |
0.0000000 |
0.0000029 |
ENSG00000160200.13 |
CBS |
FC_P |
CBS |
1.607707 |
0.0000000 |
| 2.057098e+01 |
-1.606989 |
0.3661343 |
-4.298652 |
0.0000172 |
0.0003159 |
ENSG00000100012.7 |
SEC14L3 |
FC_P |
SEC14L3 |
-1.606989 |
0.0000172 |
| 7.418793e+01 |
-1.606235 |
0.3631896 |
-4.555501 |
0.0000052 |
0.0001256 |
ENSG00000153233.8 |
PTPRR |
FC_P |
PTPRR |
-1.606235 |
0.0000052 |
| 4.971652e+01 |
-1.604928 |
0.3807218 |
-4.235823 |
0.0000228 |
0.0003938 |
ENSG00000124237.5 |
C20orf85 |
FC_P |
C20orf85 |
-1.604928 |
0.0000228 |
| 1.953535e+00 |
-1.603849 |
0.4243566 |
-3.702951 |
0.0002131 |
0.0022508 |
ENSG00000260951.1 |
RP5-978I12.1 |
FC_P |
RP5.978I12.1 |
-1.603849 |
0.0002131 |
| 5.609159e+01 |
-1.601879 |
0.3614049 |
-4.530778 |
0.0000059 |
0.0001368 |
ENSG00000162078.7 |
ZG16B |
FC_P |
ZG16B |
-1.601879 |
0.0000059 |
| 7.926429e+00 |
-1.599889 |
0.4159279 |
-3.897939 |
0.0000970 |
0.0012156 |
ENSG00000012504.9 |
NR1H4 |
FC_P |
NR1H4 |
-1.599889 |
0.0000970 |
| 1.287067e+02 |
-1.595846 |
0.4306239 |
-4.025676 |
0.0000568 |
0.0008053 |
ENSG00000166670.5 |
MMP10 |
FC_P |
MMP10 |
-1.595846 |
0.0000568 |
| 3.109340e+00 |
-1.594509 |
0.4348478 |
-4.104739 |
0.0000405 |
0.0006167 |
ENSG00000268566.1 |
RP11-687D19.1 |
FC_P |
RP11.687D19.1 |
-1.594509 |
0.0000405 |
| 4.556154e+00 |
-1.593594 |
0.4252739 |
-4.007675 |
0.0000613 |
0.0008547 |
ENSG00000200406.1 |
SNORD114-23 |
FC_P |
SNORD114.23 |
-1.593594 |
0.0000613 |
| 2.058356e+00 |
-1.585759 |
0.4259552 |
-3.720967 |
0.0001985 |
0.0021322 |
ENSG00000261480.1 |
RP11-578F21.6 |
FC_P |
RP11.578F21.6 |
-1.585759 |
0.0001985 |
| 2.436957e+01 |
-1.585755 |
0.3414095 |
-4.643281 |
0.0000034 |
0.0000905 |
ENSG00000255555.1 |
AP000857.3 |
FC_P |
AP000857.3 |
-1.585755 |
0.0000034 |
| 1.769750e+01 |
-1.584630 |
0.3374153 |
-4.718208 |
0.0000024 |
0.0000676 |
ENSG00000259590.1 |
RP11-20G13.3 |
FC_P |
RP11.20G13.3 |
-1.584630 |
0.0000024 |
| 3.037435e+00 |
-1.583881 |
0.4358179 |
-3.799113 |
0.0001452 |
0.0016698 |
ENSG00000118271.5 |
TTR |
FC_P |
TTR |
-1.583881 |
0.0001452 |
| 8.163824e+01 |
-1.583481 |
0.3471961 |
-4.632491 |
0.0000036 |
0.0000940 |
ENSG00000114204.10 |
SERPINI2 |
FC_P |
SERPINI2 |
-1.583481 |
0.0000036 |
| 2.325209e+03 |
1.583043 |
0.3464355 |
4.460830 |
0.0000082 |
0.0001769 |
ENSG00000200795.1 |
RNU4-1 |
FC_P |
RNU4.1 |
1.583043 |
0.0000082 |
| 1.152383e+02 |
-1.582556 |
0.3782377 |
-4.007530 |
0.0000614 |
0.0008549 |
ENSG00000254142.2 |
RP11-53M11.3 |
FC_P |
RP11.53M11.3 |
-1.582556 |
0.0000614 |
| 1.221791e+02 |
-1.580080 |
0.3069198 |
-5.194759 |
0.0000002 |
0.0000094 |
ENSG00000100557.5 |
C14orf105 |
FC_P |
C14orf105 |
-1.580080 |
0.0000002 |
| 4.224641e+02 |
-1.579226 |
0.3767903 |
-4.284184 |
0.0000183 |
0.0003338 |
ENSG00000137968.12 |
SLC44A5 |
FC_P |
SLC44A5 |
-1.579226 |
0.0000183 |
| 5.322447e+00 |
1.578842 |
0.2954826 |
5.289073 |
0.0000001 |
0.0000062 |
ENSG00000237264.4 |
FTH1P11 |
FC_P |
FTH1P11 |
1.578842 |
0.0000001 |
| 6.950779e+01 |
-1.578497 |
0.2519516 |
-6.424197 |
0.0000000 |
0.0000000 |
ENSG00000262529.1 |
CTA-276F8.2 |
FC_P |
CTA.276F8.2 |
-1.578497 |
0.0000000 |
| 1.245443e+01 |
1.577743 |
0.3912442 |
4.002924 |
0.0000626 |
0.0008688 |
ENSG00000199990.1 |
VTRNA1-1 |
FC_P |
VTRNA1.1 |
1.577743 |
0.0000626 |
| 1.174347e+01 |
-1.576298 |
0.3774081 |
-4.147725 |
0.0000336 |
0.0005336 |
ENSG00000242268.2 |
RP11-368I23.2 |
FC_P |
RP11.368I23.2 |
-1.576298 |
0.0000336 |
| 4.319028e+00 |
-1.574790 |
0.3953339 |
-3.960813 |
0.0000747 |
0.0009963 |
ENSG00000226409.1 |
RP11-735G4.1 |
FC_P |
RP11.735G4.1 |
-1.574790 |
0.0000747 |
| 5.758443e+00 |
-1.572808 |
0.4042124 |
-3.741475 |
0.0001829 |
0.0019958 |
ENSG00000250458.2 |
RP11-107E21.1 |
FC_P |
RP11.107E21.1 |
-1.572808 |
0.0001829 |
| 4.351673e+01 |
1.571434 |
0.3941555 |
3.622933 |
0.0002913 |
0.0028535 |
ENSG00000105697.3 |
HAMP |
FC_P |
HAMP |
1.571434 |
0.0002913 |
| 5.105132e+02 |
-1.570643 |
0.3691072 |
-4.271152 |
0.0000194 |
0.0003471 |
ENSG00000007174.13 |
DNAH9 |
FC_P |
DNAH9 |
-1.570643 |
0.0000194 |
| 4.743095e+02 |
-1.570048 |
0.3117129 |
-5.101661 |
0.0000003 |
0.0000139 |
ENSG00000154678.12 |
PDE1C |
FC_P |
PDE1C |
-1.570048 |
0.0000003 |
| 1.801050e+01 |
1.567729 |
0.3692785 |
4.004470 |
0.0000622 |
0.0008638 |
ENSG00000216866.4 |
RPS2P55 |
FC_P |
RPS2P55 |
1.567729 |
0.0000622 |
| 4.369468e+00 |
-1.566920 |
0.3462177 |
-4.455278 |
0.0000084 |
0.0001810 |
ENSG00000232524.1 |
RP11-332K15.1 |
FC_P |
RP11.332K15.1 |
-1.566920 |
0.0000084 |
| 1.880953e+01 |
-1.564362 |
0.4153869 |
-3.829827 |
0.0001282 |
0.0015080 |
ENSG00000157330.5 |
C1orf158 |
FC_P |
C1orf158 |
-1.564362 |
0.0001282 |
| 3.260924e+00 |
-1.564137 |
0.4185901 |
-3.665228 |
0.0002471 |
0.0025225 |
ENSG00000225437.1 |
RP1-257A15.1 |
FC_P |
RP1.257A15.1 |
-1.564137 |
0.0002471 |
| 5.889510e+00 |
-1.563054 |
0.3876942 |
-4.328127 |
0.0000150 |
0.0002866 |
ENSG00000234953.2 |
RP5-837I24.2 |
FC_P |
RP5.837I24.2 |
-1.563054 |
0.0000150 |
| 8.225308e+00 |
-1.562651 |
0.4247699 |
-3.673057 |
0.0002397 |
0.0024625 |
ENSG00000218476.2 |
RP11-108N13.1 |
FC_P |
RP11.108N13.1 |
-1.562651 |
0.0002397 |
| 1.671937e+01 |
-1.561706 |
0.2657241 |
-5.937160 |
0.0000000 |
0.0000003 |
ENSG00000238386.1 |
RNU7-48P |
FC_P |
RNU7.48P |
-1.561706 |
0.0000000 |
| 1.212337e+01 |
-1.561638 |
0.3452121 |
-4.532821 |
0.0000058 |
0.0001361 |
ENSG00000216022.1 |
AC068062.1 |
FC_P |
AC068062.1 |
-1.561638 |
0.0000058 |
| 1.888402e+04 |
1.560446 |
0.2773541 |
5.573725 |
0.0000000 |
0.0000017 |
ENSG00000169710.6 |
FASN |
FC_P |
FASN |
1.560446 |
0.0000000 |
| 1.365552e+01 |
-1.560404 |
0.3898377 |
-3.990055 |
0.0000661 |
0.0009061 |
ENSG00000244649.2 |
CTD-2377D24.6 |
FC_P |
CTD.2377D24.6 |
-1.560404 |
0.0000661 |
| 8.004087e+01 |
-1.559638 |
0.3716590 |
-4.190781 |
0.0000278 |
0.0004621 |
ENSG00000167858.8 |
TEKT1 |
FC_P |
TEKT1 |
-1.559638 |
0.0000278 |
| 1.895209e+01 |
1.559634 |
0.3956493 |
3.820144 |
0.0001334 |
0.0015581 |
ENSG00000258794.3 |
RP11-313F23.5 |
FC_P |
RP11.313F23.5 |
1.559634 |
0.0001334 |
| 1.201455e+02 |
-1.555338 |
0.3456697 |
-4.840664 |
0.0000013 |
0.0000407 |
ENSG00000093134.9 |
VNN3 |
FC_P |
VNN3 |
-1.555338 |
0.0000013 |
| 2.801601e+01 |
-1.554479 |
0.3317998 |
-4.699404 |
0.0000026 |
0.0000730 |
ENSG00000168589.10 |
DYNLRB2 |
FC_P |
DYNLRB2 |
-1.554479 |
0.0000026 |
| 8.455202e+00 |
-1.554318 |
0.4319698 |
-3.476687 |
0.0005077 |
0.0043667 |
ENSG00000261713.2 |
SSTR5-AS1 |
FC_P |
SSTR5.AS1 |
-1.554318 |
0.0005077 |
| 1.808876e+01 |
-1.553342 |
0.3238830 |
-4.779411 |
0.0000018 |
0.0000523 |
ENSG00000239084.1 |
snoU13 |
FC_P |
snoU13.1 |
-1.553342 |
0.0000018 |
| 1.611715e+01 |
-1.552972 |
0.3518433 |
-4.426809 |
0.0000096 |
0.0002018 |
ENSG00000184617.9 |
ZNF840 |
FC_P |
ZNF840 |
-1.552972 |
0.0000096 |
| 4.352341e+00 |
-1.551216 |
0.4255485 |
-3.692417 |
0.0002221 |
0.0023205 |
ENSG00000200480.1 |
SNORD114-28 |
FC_P |
SNORD114.28 |
-1.551216 |
0.0002221 |
| 9.153142e+01 |
1.551193 |
0.2290808 |
6.707414 |
0.0000000 |
0.0000000 |
ENSG00000141965.3 |
FEM1A |
FC_P |
FEM1A |
1.551193 |
0.0000000 |
| 6.582343e+00 |
-1.550812 |
0.4198405 |
-3.979807 |
0.0000690 |
0.0009366 |
ENSG00000206889.1 |
RNU6-1200P |
FC_P |
RNU6.1200P |
-1.550812 |
0.0000690 |
| 3.372070e+02 |
-1.550550 |
0.3766542 |
-4.103474 |
0.0000407 |
0.0006189 |
ENSG00000018625.10 |
ATP1A2 |
FC_P |
ATP1A2 |
-1.550550 |
0.0000407 |
| 1.618156e+01 |
-1.550077 |
0.3671963 |
-4.209330 |
0.0000256 |
0.0004327 |
ENSG00000255160.1 |
RP11-428C19.5 |
FC_P |
RP11.428C19.5 |
-1.550077 |
0.0000256 |
| 6.257576e+01 |
-1.548874 |
0.3557593 |
-4.323086 |
0.0000154 |
0.0002909 |
ENSG00000188993.3 |
LRRC66 |
FC_P |
LRRC66 |
-1.548874 |
0.0000154 |
| 4.963583e+01 |
-1.547897 |
0.3744388 |
-4.510814 |
0.0000065 |
0.0001471 |
ENSG00000165078.7 |
CPA6 |
FC_P |
CPA6 |
-1.547897 |
0.0000065 |
| 4.597827e+00 |
-1.546696 |
0.3739296 |
-4.174998 |
0.0000298 |
0.0004876 |
ENSG00000228842.2 |
PCDH9-AS2 |
FC_P |
PCDH9.AS2 |
-1.546696 |
0.0000298 |
| 3.402624e+00 |
-1.545968 |
0.3609463 |
-4.219416 |
0.0000245 |
0.0004177 |
ENSG00000251722.1 |
RNU5E-3P |
FC_P |
RNU5E.3P |
-1.545968 |
0.0000245 |
| 1.592318e+01 |
-1.544850 |
0.3712243 |
-4.156073 |
0.0000324 |
0.0005176 |
ENSG00000255308.1 |
RP11-428C19.4 |
FC_P |
RP11.428C19.4 |
-1.544850 |
0.0000324 |
| 5.445472e+00 |
-1.544404 |
0.3963451 |
-3.992229 |
0.0000655 |
0.0008999 |
ENSG00000272958.1 |
CMP21-97G8.2 |
FC_P |
CMP21.97G8.2 |
-1.544404 |
0.0000655 |
| 9.734185e+01 |
-1.544195 |
0.4137684 |
-3.818666 |
0.0001342 |
0.0015650 |
ENSG00000108242.8 |
CYP2C18 |
FC_P |
CYP2C18 |
-1.544195 |
0.0001342 |
| 1.362036e+01 |
-1.542546 |
0.2748294 |
-5.607466 |
0.0000000 |
0.0000014 |
ENSG00000252294.1 |
RNU6-589P |
FC_P |
RNU6.589P |
-1.542546 |
0.0000000 |
| 3.069838e+01 |
-1.542401 |
0.2779478 |
-5.648466 |
0.0000000 |
0.0000012 |
ENSG00000207967.1 |
MIR620 |
FC_P |
MIR620 |
-1.542401 |
0.0000000 |
| 2.283738e+01 |
-1.538561 |
0.3643478 |
-4.249326 |
0.0000214 |
0.0003750 |
ENSG00000230062.4 |
ANKRD66 |
FC_P |
ANKRD66 |
-1.538561 |
0.0000214 |
| 8.107794e+00 |
-1.537181 |
0.3564991 |
-4.454194 |
0.0000084 |
0.0001817 |
ENSG00000263652.1 |
MIR548AX |
FC_P |
MIR548AX |
-1.537181 |
0.0000084 |
| 9.732619e+01 |
-1.537131 |
0.3473575 |
-4.390701 |
0.0000113 |
0.0002281 |
ENSG00000227954.2 |
RP3-323P13.2 |
FC_P |
RP3.323P13.2 |
-1.537131 |
0.0000113 |
| 3.673474e+01 |
-1.535843 |
0.2572689 |
-6.068152 |
0.0000000 |
0.0000002 |
ENSG00000207286.1 |
Y_RNA |
FC_P |
Y_RNA.2 |
-1.535843 |
0.0000000 |
| 1.056367e+01 |
1.534598 |
0.4376792 |
3.524911 |
0.0004236 |
0.0038063 |
ENSG00000227599.1 |
RP4-753D4.2 |
FC_P |
RP4.753D4.2 |
1.534598 |
0.0004236 |
| 1.157003e+01 |
1.534315 |
0.3457975 |
4.402396 |
0.0000107 |
0.0002191 |
ENSG00000214784.4 |
AC010468.1 |
FC_P |
AC010468.1 |
1.534315 |
0.0000107 |
| 1.470905e+03 |
1.531104 |
0.4038813 |
4.146028 |
0.0000338 |
0.0005373 |
ENSG00000105825.7 |
TFPI2 |
FC_P |
TFPI2 |
1.531104 |
0.0000338 |
| 2.372372e+01 |
-1.531027 |
0.3917049 |
-3.327857 |
0.0008752 |
0.0066873 |
ENSG00000164756.8 |
SLC30A8 |
FC_P |
SLC30A8 |
-1.531027 |
0.0008752 |
| 1.126816e+01 |
-1.530888 |
0.2796606 |
-5.488856 |
0.0000000 |
0.0000025 |
ENSG00000252686.1 |
RNU6-1234P |
FC_P |
RNU6.1234P |
-1.530888 |
0.0000000 |
| 2.088821e+01 |
-1.529041 |
0.3241820 |
-4.758227 |
0.0000020 |
0.0000574 |
ENSG00000261496.1 |
RP13-514E23.1 |
FC_P |
RP13.514E23.1 |
-1.529041 |
0.0000020 |
| 2.019348e+02 |
-1.528896 |
0.3570717 |
-4.258705 |
0.0000206 |
0.0003615 |
ENSG00000197520.6 |
FAM177B |
FC_P |
FAM177B |
-1.528896 |
0.0000206 |
| 9.193095e+00 |
-1.528844 |
0.4189109 |
-3.552773 |
0.0003812 |
0.0035076 |
ENSG00000210195.2 |
MT-TT |
FC_P |
MT.TT |
-1.528844 |
0.0003812 |
| 6.062482e+00 |
-1.526600 |
0.3388602 |
-4.489676 |
0.0000071 |
0.0001590 |
ENSG00000200508.1 |
Y_RNA |
FC_P |
Y_RNA.3 |
-1.526600 |
0.0000071 |
| 9.732164e+01 |
1.524814 |
0.4360688 |
3.339370 |
0.0008397 |
0.0064788 |
ENSG00000183242.7 |
WT1-AS |
FC_P |
WT1.AS |
1.524814 |
0.0008397 |
| 2.548883e+00 |
-1.523768 |
0.4326909 |
-3.582397 |
0.0003405 |
0.0032126 |
ENSG00000239184.1 |
RNA5SP269 |
FC_P |
RNA5SP269 |
-1.523768 |
0.0003405 |
| 1.434056e+01 |
-1.522882 |
0.3702719 |
-4.199357 |
0.0000268 |
0.0004485 |
ENSG00000254959.2 |
INMT-FAM188B |
FC_P |
INMT.FAM188B |
-1.522882 |
0.0000268 |
| 1.113133e+01 |
-1.521503 |
0.3217797 |
-4.858058 |
0.0000012 |
0.0000381 |
ENSG00000238388.1 |
snoU13 |
FC_P |
snoU13.2 |
-1.521503 |
0.0000012 |
| 5.203878e+01 |
-1.518197 |
0.3754967 |
-4.148732 |
0.0000334 |
0.0005315 |
ENSG00000229233.1 |
AC011891.5 |
FC_P |
AC011891.5 |
-1.518197 |
0.0000334 |
| 5.847675e+00 |
-1.517882 |
0.3598884 |
-4.384626 |
0.0000116 |
0.0002336 |
ENSG00000252210.1 |
Y_RNA |
FC_P |
Y_RNA.4 |
-1.517882 |
0.0000116 |
| 4.965776e+00 |
1.517821 |
0.3416592 |
4.413374 |
0.0000102 |
0.0002108 |
ENSG00000231977.1 |
RP5-963E22.4 |
FC_P |
RP5.963E22.4 |
1.517821 |
0.0000102 |
| 3.453608e+00 |
-1.516391 |
0.4331745 |
-3.439144 |
0.0005836 |
0.0048748 |
ENSG00000225417.1 |
RP5-1178H5.2 |
FC_P |
RP5.1178H5.2 |
-1.516391 |
0.0005836 |
| 2.143091e+00 |
-1.516257 |
0.4319315 |
-3.384969 |
0.0007119 |
0.0056858 |
ENSG00000231720.1 |
RP11-568A7.3 |
FC_P |
RP11.568A7.3 |
-1.516257 |
0.0007119 |
| 7.190674e+01 |
-1.515836 |
0.3226988 |
-4.691450 |
0.0000027 |
0.0000749 |
ENSG00000089101.13 |
C20orf26 |
FC_P |
C20orf26 |
-1.515836 |
0.0000027 |
| 2.583663e+01 |
-1.514908 |
0.2371353 |
-6.418420 |
0.0000000 |
0.0000000 |
ENSG00000252496.1 |
RNA5SP33 |
FC_P |
RNA5SP33 |
-1.514908 |
0.0000000 |
| 2.505869e+01 |
-1.514818 |
0.3851561 |
-3.905180 |
0.0000942 |
0.0011889 |
ENSG00000263429.3 |
LINC00675 |
FC_P |
LINC00675 |
-1.514818 |
0.0000942 |
| 1.118913e+01 |
-1.514293 |
0.2994027 |
-5.009731 |
0.0000005 |
0.0000204 |
ENSG00000167355.3 |
AC104389.28 |
FC_P |
AC104389.28 |
-1.514293 |
0.0000005 |
| 1.145388e+01 |
-1.513706 |
0.3632942 |
-4.049824 |
0.0000513 |
0.0007452 |
ENSG00000233005.1 |
AC067959.1 |
FC_P |
AC067959.1 |
-1.513706 |
0.0000513 |
| 1.016584e+02 |
-1.510691 |
0.2915612 |
-5.178667 |
0.0000002 |
0.0000100 |
ENSG00000197168.7 |
NEK5 |
FC_P |
NEK5 |
-1.510691 |
0.0000002 |
| 4.730575e+00 |
-1.508917 |
0.4280495 |
-3.435003 |
0.0005925 |
0.0049294 |
ENSG00000258765.1 |
RP11-692C24.2 |
FC_P |
RP11.692C24.2 |
-1.508917 |
0.0005925 |
| 9.642318e+00 |
-1.508566 |
0.3672604 |
-4.086680 |
0.0000438 |
0.0006550 |
ENSG00000242810.1 |
MRPL42P6 |
FC_P |
MRPL42P6 |
-1.508566 |
0.0000438 |
| 4.530483e+01 |
-1.508454 |
0.4064216 |
-3.763919 |
0.0001673 |
0.0018623 |
ENSG00000162598.9 |
C1orf87 |
FC_P |
C1orf87 |
-1.508454 |
0.0001673 |
| 5.599512e+00 |
-1.508323 |
0.3003748 |
-4.984584 |
0.0000006 |
0.0000226 |
ENSG00000222578.1 |
RNA5SP345 |
FC_P |
RNA5SP345 |
-1.508323 |
0.0000006 |
| 1.726251e+00 |
-1.506713 |
0.4357671 |
-3.528516 |
0.0004179 |
0.0037723 |
ENSG00000230258.2 |
AC002539.1 |
FC_P |
AC002539.1 |
-1.506713 |
0.0004179 |
| 3.347572e+00 |
-1.505292 |
0.3660678 |
-4.070770 |
0.0000469 |
0.0006917 |
ENSG00000242180.2 |
OR51B5 |
FC_P |
OR51B5 |
-1.505292 |
0.0000469 |
| 3.816121e+00 |
-1.505219 |
0.3516150 |
-4.263974 |
0.0000201 |
0.0003557 |
ENSG00000273389.1 |
RP13-514E23.2 |
FC_P |
RP13.514E23.2 |
-1.505219 |
0.0000201 |
| 5.342284e+00 |
-1.504836 |
0.3511695 |
-4.359477 |
0.0000130 |
0.0002569 |
ENSG00000207267.1 |
RNU6-1081P |
FC_P |
RNU6.1081P |
-1.504836 |
0.0000130 |
| 5.959016e+00 |
-1.504820 |
0.3902608 |
-3.812581 |
0.0001375 |
0.0015985 |
ENSG00000258162.1 |
RP11-315E17.1 |
FC_P |
RP11.315E17.1 |
-1.504820 |
0.0001375 |
| 8.870222e+01 |
-1.502227 |
0.3206199 |
-4.729730 |
0.0000022 |
0.0000644 |
ENSG00000166596.10 |
WDR16 |
FC_P |
WDR16 |
-1.502227 |
0.0000022 |
Pathway enrichment analysis fGSEA
Low BAP1 is the reference. When BAP1 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='BAP1 low vs high')

kable(fgp)
| HALLMARK_MYC_TARGETS_V2 |
0.0019841 |
0.0031048 |
0.7514702 |
2.985838 |
0 |
57 |
up |
| HALLMARK_MYC_TARGETS_V1 |
0.0019120 |
0.0031048 |
0.5951325 |
2.882789 |
0 |
189 |
up |
| HALLMARK_DNA_REPAIR |
0.0018587 |
0.0031048 |
0.5669329 |
2.639105 |
0 |
141 |
up |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY |
0.0019920 |
0.0031048 |
0.6926141 |
2.626220 |
0 |
46 |
up |
| HALLMARK_P53_PATHWAY |
0.0018975 |
0.0031048 |
0.5354251 |
2.595026 |
0 |
190 |
up |
| HALLMARK_G2M_CHECKPOINT |
0.0019120 |
0.0031048 |
0.5121996 |
2.478671 |
0 |
187 |
up |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE |
0.0019569 |
0.0031048 |
0.5601328 |
2.470739 |
0 |
103 |
up |
| HALLMARK_E2F_TARGETS |
0.0019084 |
0.0031048 |
0.5029007 |
2.432800 |
0 |
191 |
up |
| HALLMARK_UV_RESPONSE_UP |
0.0018484 |
0.0031048 |
0.5152321 |
2.422013 |
0 |
147 |
up |
| HALLMARK_MITOTIC_SPINDLE |
0.0018797 |
0.0031048 |
0.4951850 |
2.409677 |
0 |
195 |
up |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION |
0.0018939 |
0.0031048 |
0.4960800 |
2.384563 |
0 |
175 |
up |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0018797 |
0.0031048 |
0.4853719 |
2.361925 |
0 |
195 |
up |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0019417 |
0.0031048 |
0.5260215 |
2.295795 |
0 |
93 |
up |
| HALLMARK_PI3K_AKT_MTOR_SIGNALING |
0.0019569 |
0.0031048 |
0.5143544 |
2.268811 |
0 |
103 |
up |
| HALLMARK_INTERFERON_GAMMA_RESPONSE |
0.0018868 |
0.0031048 |
0.4644912 |
2.256368 |
0 |
194 |
up |
| HALLMARK_MTORC1_SIGNALING |
0.0018975 |
0.0031048 |
0.4637870 |
2.247821 |
0 |
190 |
up |
| HALLMARK_APOPTOSIS |
0.0018519 |
0.0031048 |
0.4714723 |
2.227226 |
0 |
155 |
up |
| HALLMARK_GLYCOLYSIS |
0.0019120 |
0.0031048 |
0.4162795 |
2.014886 |
0 |
188 |
up |
| HALLMARK_APICAL_JUNCTION |
0.0019120 |
0.0031048 |
0.4133881 |
2.002429 |
0 |
189 |
up |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0019120 |
0.0031048 |
0.4081824 |
1.975304 |
0 |
187 |
up |
| HALLMARK_ADIPOGENESIS |
0.0019084 |
0.0031048 |
0.4086975 |
1.969521 |
0 |
183 |
up |
| HALLMARK_WNT_BETA_CATENIN_SIGNALING |
0.0020408 |
0.0031048 |
0.5188031 |
1.923844 |
0 |
42 |
up |
| HALLMARK_INFLAMMATORY_RESPONSE |
0.0018868 |
0.0031048 |
0.3906481 |
1.897625 |
0 |
193 |
up |
| HALLMARK_MYOGENESIS |
0.0018975 |
0.0031048 |
0.3863939 |
1.872722 |
0 |
190 |
up |
| HALLMARK_IL6_JAK_STAT3_SIGNALING |
0.0020492 |
0.0031048 |
0.4396043 |
1.859896 |
0 |
82 |
up |
| HALLMARK_ESTROGEN_RESPONSE_LATE |
0.0018868 |
0.0031048 |
0.3751503 |
1.822342 |
0 |
193 |
up |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS |
0.0019724 |
0.0031048 |
0.4383596 |
1.811611 |
0 |
69 |
up |
| HALLMARK_HEME_METABOLISM |
0.0019194 |
0.0031048 |
0.3709272 |
1.782191 |
0 |
179 |
up |
| HALLMARK_ESTROGEN_RESPONSE_EARLY |
0.0019084 |
0.0031048 |
0.3670963 |
1.775841 |
0 |
191 |
up |
| HALLMARK_HYPOXIA |
0.0019048 |
0.0031048 |
0.3686240 |
1.771905 |
0 |
180 |
up |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='BAP1 low vs high')

kable(fgp)
| chr19p13 |
0.0018657 |
0.0059037 |
0.7507847 |
4.048989 |
0 |
544 |
up |
| chr9q34 |
0.0018553 |
0.0059037 |
0.7295889 |
3.578502 |
0 |
210 |
up |
| chr17q25 |
0.0018762 |
0.0059037 |
0.6672525 |
3.260381 |
0 |
202 |
up |
| chr3p21 |
0.0018657 |
0.0059037 |
0.6541574 |
3.210588 |
0 |
211 |
up |
| chr19q13 |
0.0018149 |
0.0059037 |
0.5602329 |
3.098032 |
0 |
769 |
up |
| chr16p11 |
0.0019157 |
0.0059037 |
0.6603864 |
3.012990 |
0 |
120 |
up |
| chr11q13 |
0.0018450 |
0.0059037 |
0.5918730 |
3.009112 |
0 |
290 |
up |
| chr16q24 |
0.0020040 |
0.0059037 |
0.6331231 |
2.733117 |
0 |
92 |
up |
| chr1p31 |
0.0020833 |
0.0059037 |
-0.5831812 |
-2.646177 |
0 |
120 |
down |
| chr7p22 |
0.0020325 |
0.0059037 |
0.6055466 |
2.592822 |
0 |
85 |
up |
| chr4p16 |
0.0019194 |
0.0059037 |
0.5684632 |
2.582216 |
0 |
118 |
up |
| chr22q13 |
0.0018762 |
0.0059037 |
0.5237570 |
2.573764 |
0 |
215 |
up |
| chr1q22 |
0.0020790 |
0.0059037 |
0.6570445 |
2.547734 |
0 |
53 |
up |
| chr17p13 |
0.0018149 |
0.0059037 |
0.5034765 |
2.512875 |
0 |
236 |
up |
| chr7q36 |
0.0019920 |
0.0059037 |
0.5704783 |
2.511936 |
0 |
101 |
up |
| chr20q11 |
0.0019724 |
0.0059037 |
0.5282767 |
2.489806 |
0 |
159 |
up |
| chr17q21 |
0.0018450 |
0.0059037 |
0.4838084 |
2.440629 |
0 |
271 |
up |
| chr12q21 |
0.0019685 |
0.0059037 |
-0.5970674 |
-2.440323 |
0 |
66 |
down |
| chr20q13 |
0.0018382 |
0.0059037 |
0.4797197 |
2.416472 |
0 |
265 |
up |
| chr12p12 |
0.0019455 |
0.0059037 |
-0.5717705 |
-2.331402 |
0 |
65 |
down |
| chr7q22 |
0.0019724 |
0.0059037 |
0.4965144 |
2.329010 |
0 |
153 |
up |
| chr5q35 |
0.0019380 |
0.0059037 |
0.5031428 |
2.328435 |
0 |
135 |
up |
| chr9p13 |
0.0018939 |
0.0059037 |
0.5079495 |
2.301112 |
0 |
113 |
up |
| chr5p13 |
0.0019455 |
0.0059037 |
-0.5355983 |
-2.298951 |
0 |
84 |
down |
| chr12q24 |
0.0018587 |
0.0059037 |
0.4558662 |
2.279257 |
0 |
250 |
up |
| chr1q21 |
0.0018762 |
0.0059037 |
0.4685764 |
2.275820 |
0 |
191 |
up |
| chr8q21 |
0.0019960 |
0.0059037 |
-0.5192316 |
-2.250271 |
0 |
90 |
down |
| chr8q22 |
0.0019455 |
0.0059037 |
-0.5240361 |
-2.249322 |
0 |
84 |
down |
| chr22q11 |
0.0018868 |
0.0059037 |
0.4528396 |
2.220897 |
0 |
214 |
up |
| chr16p13 |
0.0018282 |
0.0059037 |
0.4379570 |
2.213789 |
0 |
272 |
up |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='BAP1 low vs high')

kable(fgp)
| GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN |
0.0019802 |
0.0079622 |
0.7426209 |
3.761729 |
0 |
308 |
up |
| LU_EZH2_TARGETS_UP |
0.0019194 |
0.0079622 |
0.6838918 |
3.395229 |
0 |
257 |
up |
| SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP |
0.0018832 |
0.0079622 |
0.6407552 |
3.372171 |
0 |
444 |
up |
| RICKMAN_METASTASIS_DN |
0.0019305 |
0.0079622 |
0.6842922 |
3.371849 |
0 |
246 |
up |
| MARTENS_TRETINOIN_RESPONSE_DN |
0.0018182 |
0.0079622 |
0.6052181 |
3.357854 |
0 |
722 |
up |
| MARTENS_BOUND_BY_PML_RARA_FUSION |
0.0019493 |
0.0079622 |
0.6332474 |
3.307524 |
0 |
418 |
up |
| REACTOME_RRNA_PROCESSING |
0.0019305 |
0.0079622 |
0.6887952 |
3.285542 |
0 |
184 |
up |
| DACOSTA_UV_RESPONSE_VIA_ERCC3_UP |
0.0019342 |
0.0079622 |
0.6484617 |
3.278440 |
0 |
294 |
up |
| KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP |
0.0018519 |
0.0079622 |
0.5935414 |
3.275786 |
0 |
693 |
up |
| WELCSH_BRCA1_TARGETS_DN |
0.0019608 |
0.0079622 |
0.7266808 |
3.247569 |
0 |
127 |
up |
| ENK_UV_RESPONSE_KERATINOCYTE_UP |
0.0018484 |
0.0079622 |
0.6087051 |
3.238186 |
0 |
487 |
up |
| KIM_ALL_DISORDERS_DURATION_CORR_DN |
0.0019569 |
0.0079622 |
0.7124291 |
3.230082 |
0 |
134 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION |
0.0020040 |
0.0079622 |
0.7715309 |
3.228295 |
0 |
86 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION |
0.0019531 |
0.0079622 |
0.7426040 |
3.227236 |
0 |
112 |
up |
| HSIAO_HOUSEKEEPING_GENES |
0.0019231 |
0.0079622 |
0.6232810 |
3.213668 |
0 |
362 |
up |
| SANSOM_APC_TARGETS_REQUIRE_MYC |
0.0019960 |
0.0079622 |
0.6661419 |
3.211729 |
0 |
209 |
up |
| KEGG_RIBOSOME |
0.0020121 |
0.0079622 |
0.7683390 |
3.197411 |
0 |
81 |
up |
| SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC |
0.0019608 |
0.0079622 |
0.7394982 |
3.183014 |
0 |
101 |
up |
| LI_DCP2_BOUND_MRNA |
0.0020080 |
0.0079622 |
0.7644617 |
3.165287 |
0 |
78 |
up |
| REACTOME_INFLUENZA_INFECTION |
0.0019646 |
0.0079622 |
0.6891440 |
3.159990 |
0 |
145 |
up |
| REACTOME_NONSENSE_MEDIATED_DECAY_NMD |
0.0019685 |
0.0079622 |
0.7298401 |
3.151569 |
0 |
108 |
up |
| REACTOME_METABOLISM_OF_RNA |
0.0018975 |
0.0079622 |
0.5721733 |
3.120585 |
0 |
626 |
up |
| REACTOME_TRANSLATION |
0.0019194 |
0.0079622 |
0.6252563 |
3.108811 |
0 |
262 |
up |
| REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY |
0.0019646 |
0.0079622 |
0.7258810 |
3.084952 |
0 |
94 |
up |
| REACTOME_SELENOAMINO_ACID_METABOLISM |
0.0019685 |
0.0079622 |
0.7129670 |
3.068063 |
0 |
102 |
up |
| KASLER_HDAC7_TARGETS_1_UP |
0.0019157 |
0.0079622 |
0.6493167 |
3.067242 |
0 |
168 |
up |
| AMIT_EGF_RESPONSE_480_HELA |
0.0019685 |
0.0079622 |
0.6600758 |
3.051282 |
0 |
151 |
up |
| LOPEZ_MBD_TARGETS |
0.0017857 |
0.0079622 |
0.5425486 |
3.048602 |
0 |
885 |
up |
| CAIRO_HEPATOBLASTOMA_CLASSES_UP |
0.0018587 |
0.0079622 |
0.5635591 |
3.046571 |
0 |
560 |
up |
| SANSOM_APC_MYC_TARGETS |
0.0019531 |
0.0079622 |
0.6241811 |
3.035292 |
0 |
224 |
up |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='BAP1 low vs high')

kable(fgp)
| SUPT20H_TARGET_GENES |
0.0018587 |
0.0067637 |
0.5587984 |
3.191683 |
0 |
1169 |
up |
| CEBPZ_TARGET_GENES |
0.0018116 |
0.0067637 |
0.5487399 |
3.162717 |
0 |
1304 |
up |
| HDGF_TARGET_GENES |
0.0018939 |
0.0067637 |
0.5645479 |
3.132154 |
0 |
776 |
up |
| SETD7_TARGET_GENES |
0.0018868 |
0.0067637 |
0.5641538 |
3.130648 |
0 |
786 |
up |
| MIR4492 |
0.0018832 |
0.0067637 |
0.5958888 |
3.110372 |
0 |
372 |
up |
| ZNF436_TARGET_GENES |
0.0019157 |
0.0067637 |
0.5883892 |
3.105689 |
0 |
429 |
up |
| FXR1_TARGET_GENES |
0.0018553 |
0.0067637 |
0.5482645 |
3.098145 |
0 |
1002 |
up |
| NFKBIA_TARGET_GENES |
0.0018051 |
0.0067637 |
0.5457988 |
3.095049 |
0 |
1011 |
up |
| MIR4283 |
0.0019417 |
0.0067637 |
0.6330661 |
3.051605 |
0 |
194 |
up |
| MIR6825_5P |
0.0019011 |
0.0067637 |
0.5845721 |
3.051434 |
0 |
379 |
up |
| THAP1_TARGET_GENES |
0.0018832 |
0.0067637 |
0.5222676 |
3.041789 |
0 |
1667 |
up |
| ADNP_TARGET_GENES |
0.0018622 |
0.0067637 |
0.5587294 |
3.033462 |
0 |
543 |
up |
| KLF14_TARGET_GENES |
0.0019268 |
0.0067637 |
0.6176392 |
3.030428 |
0 |
215 |
up |
| MIR4763_3P |
0.0019531 |
0.0067637 |
0.6142792 |
3.029706 |
0 |
225 |
up |
| RBM34_TARGET_GENES |
0.0018519 |
0.0067637 |
0.5396694 |
3.015813 |
0 |
846 |
up |
| MIR4731_5P |
0.0019048 |
0.0067637 |
0.6012254 |
2.992164 |
0 |
237 |
up |
| KAT5_TARGET_GENES |
0.0018622 |
0.0067637 |
0.5386702 |
2.990838 |
0 |
768 |
up |
| MIR1207_5P |
0.0018553 |
0.0067637 |
0.5815773 |
2.966539 |
0 |
301 |
up |
| EPC1_TARGET_GENES |
0.0019048 |
0.0067637 |
0.5730291 |
2.952376 |
0 |
332 |
up |
| KLF13_TARGET_GENES |
0.0018692 |
0.0067637 |
0.5059913 |
2.952132 |
0 |
1766 |
up |
| MIR486_3P |
0.0019455 |
0.0067637 |
0.6396048 |
2.950824 |
0 |
153 |
up |
| MCM2_TARGET_GENES |
0.0020202 |
0.0067637 |
0.7176487 |
2.941038 |
0 |
76 |
up |
| CIITA_TARGET_GENES |
0.0018315 |
0.0067637 |
0.5172643 |
2.936420 |
0 |
1039 |
up |
| MIR4505 |
0.0019380 |
0.0067637 |
0.5921316 |
2.936374 |
0 |
235 |
up |
| MIR423_5P |
0.0019231 |
0.0067637 |
0.6522103 |
2.934732 |
0 |
129 |
up |
| CDC73_TARGET_GENES |
0.0018762 |
0.0067637 |
0.5417707 |
2.933345 |
0 |
538 |
up |
| MIR6721_5P |
0.0018484 |
0.0067637 |
0.5723532 |
2.925491 |
0 |
308 |
up |
| ZNF92_TARGET_GENES |
0.0018727 |
0.0067637 |
0.5109499 |
2.920817 |
0 |
1183 |
up |
| JDP2_TARGET_GENES |
0.0018484 |
0.0067637 |
0.4999463 |
2.915312 |
0 |
1661 |
up |
| MIR6883_5P |
0.0018975 |
0.0067637 |
0.5551820 |
2.897276 |
0 |
380 |
up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='BAP1 low vs high')

kable(fgp)
| MORF_UBE2I |
0.0019493 |
0.0051258 |
0.7133588 |
3.527450 |
0 |
219 |
up |
| MORF_PHB |
0.0019120 |
0.0051258 |
0.7680946 |
3.476173 |
0 |
113 |
up |
| MORF_NME2 |
0.0019342 |
0.0051258 |
0.7289640 |
3.408664 |
0 |
141 |
up |
| MORF_NPM1 |
0.0019608 |
0.0051258 |
0.7185991 |
3.381004 |
0 |
149 |
up |
| MORF_CSNK2B |
0.0018832 |
0.0051258 |
0.6701245 |
3.380885 |
0 |
258 |
up |
| MORF_ACTG1 |
0.0019380 |
0.0051258 |
0.7308713 |
3.366872 |
0 |
127 |
up |
| MORF_AP2M1 |
0.0019194 |
0.0051258 |
0.6851841 |
3.362316 |
0 |
203 |
up |
| MORF_ANP32B |
0.0020161 |
0.0051258 |
0.6985141 |
3.358730 |
0 |
183 |
up |
| MORF_AATF |
0.0019802 |
0.0051258 |
0.6924533 |
3.357759 |
0 |
191 |
up |
| MORF_FBL |
0.0019194 |
0.0051258 |
0.7240208 |
3.345283 |
0 |
129 |
up |
| MORF_RAD23A |
0.0018622 |
0.0051258 |
0.6429129 |
3.318616 |
0 |
304 |
up |
| MORF_DDB1 |
0.0019268 |
0.0051258 |
0.6666799 |
3.308989 |
0 |
226 |
up |
| MORF_EIF3S2 |
0.0019417 |
0.0051258 |
0.6676889 |
3.306004 |
0 |
220 |
up |
| MORF_TPT1 |
0.0019531 |
0.0051258 |
0.7594675 |
3.305835 |
0 |
92 |
up |
| MORF_MAP2K2 |
0.0019531 |
0.0051258 |
0.7265419 |
3.292324 |
0 |
117 |
up |
| MORF_IKBKG |
0.0019493 |
0.0051258 |
0.7139560 |
3.283910 |
0 |
126 |
up |
| MORF_DAP3 |
0.0020243 |
0.0051258 |
0.6815812 |
3.274829 |
0 |
179 |
up |
| MORF_RAN |
0.0019157 |
0.0051258 |
0.6511978 |
3.254191 |
0 |
239 |
up |
| MORF_RPA2 |
0.0020161 |
0.0051258 |
0.6793347 |
3.253192 |
0 |
176 |
up |
| GNF2_EIF3S6 |
0.0019194 |
0.0051258 |
0.7163001 |
3.228532 |
0 |
110 |
up |
| MORF_BUB3 |
0.0019194 |
0.0051258 |
0.6462123 |
3.226195 |
0 |
243 |
up |
| GCM_CSNK2B |
0.0019531 |
0.0051258 |
0.7497331 |
3.214405 |
0 |
87 |
up |
| MODULE_83 |
0.0018622 |
0.0051258 |
0.6244084 |
3.199685 |
0 |
290 |
up |
| MORF_HDAC1 |
0.0019048 |
0.0051258 |
0.6413447 |
3.197034 |
0 |
231 |
up |
| GCM_TPT1 |
0.0020202 |
0.0051258 |
0.7992662 |
3.166444 |
0 |
59 |
up |
| MORF_CTBP1 |
0.0020000 |
0.0051258 |
0.6673619 |
3.164312 |
0 |
159 |
up |
| MODULE_257 |
0.0019724 |
0.0051258 |
0.6704206 |
3.155993 |
0 |
150 |
up |
| MORF_PPP1CA |
0.0020161 |
0.0051258 |
0.6665923 |
3.141889 |
0 |
153 |
up |
| MORF_G22P1 |
0.0020243 |
0.0051258 |
0.6599471 |
3.124111 |
0 |
158 |
up |
| MORF_GNB1 |
0.0018832 |
0.0051258 |
0.6137062 |
3.123175 |
0 |
274 |
up |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='BAP1 low vs high')

kable(fgp)
| GO_VIRAL_GENE_EXPRESSION |
0.0019685 |
0.0101779 |
0.7022003 |
3.368700 |
0 |
185 |
up |
| GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAY |
0.0019802 |
0.0101779 |
0.7260161 |
3.245483 |
0 |
114 |
up |
| GO_RIBOSOME_BIOGENESIS |
0.0020534 |
0.0101779 |
0.6381337 |
3.200949 |
0 |
259 |
up |
| GO_STRUCTURAL_CONSTITUENT_OF_RIBOSOME |
0.0020284 |
0.0101779 |
0.6778943 |
3.163143 |
0 |
152 |
up |
| GO_TRANSLATIONAL_INITIATION |
0.0019920 |
0.0101779 |
0.6601471 |
3.149390 |
0 |
179 |
up |
| GO_RIBONUCLEOPROTEIN_COMPLEX |
0.0019531 |
0.0101779 |
0.5721550 |
3.144505 |
0 |
630 |
up |
| GO_RIBOSOMAL_SUBUNIT |
0.0020040 |
0.0101779 |
0.6578464 |
3.128156 |
0 |
172 |
up |
| GO_CYTOSOLIC_RIBOSOME |
0.0019157 |
0.0101779 |
0.7178149 |
3.109921 |
0 |
95 |
up |
| GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS |
0.0019646 |
0.0101779 |
0.5908406 |
3.099263 |
0 |
382 |
up |
| GO_LARGE_RIBOSOMAL_SUBUNIT |
0.0019960 |
0.0101779 |
0.7027448 |
3.096872 |
0 |
108 |
up |
| GO_CYTOSOLIC_LARGE_RIBOSOMAL_SUBUNIT |
0.0020619 |
0.0101779 |
0.8017296 |
3.086059 |
0 |
53 |
up |
| GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE |
0.0019493 |
0.0101779 |
0.7162438 |
3.082829 |
0 |
94 |
up |
| GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS |
0.0019920 |
0.0101779 |
0.7665020 |
3.077570 |
0 |
62 |
up |
| GO_RIBOSOME |
0.0019841 |
0.0101779 |
0.6254103 |
3.050640 |
0 |
211 |
up |
| GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM |
0.0019417 |
0.0101779 |
0.6894414 |
3.039172 |
0 |
106 |
up |
| GO_RRNA_METABOLIC_PROCESS |
0.0020000 |
0.0101779 |
0.6305050 |
3.028541 |
0 |
195 |
up |
| GO_PROTEIN_TARGETING_TO_MEMBRANE |
0.0020040 |
0.0101779 |
0.6273435 |
2.987217 |
0 |
173 |
up |
| GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS |
0.0020080 |
0.0101779 |
0.6203842 |
2.964279 |
0 |
189 |
up |
| GO_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS |
0.0019194 |
0.0101779 |
0.5279694 |
2.959300 |
0 |
859 |
up |
| GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE |
0.0019646 |
0.0101779 |
0.5770295 |
2.956024 |
0 |
296 |
up |
| GO_NUCLEOLUS |
0.0018622 |
0.0101779 |
0.5254808 |
2.944526 |
0 |
837 |
up |
| GO_PRERIBOSOME |
0.0019841 |
0.0101779 |
0.7164599 |
2.937476 |
0 |
71 |
up |
| GO_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM |
0.0019531 |
0.0101779 |
0.6456861 |
2.929843 |
0 |
128 |
up |
| GO_MRNA_METABOLIC_PROCESS |
0.0019231 |
0.0101779 |
0.5267203 |
2.924927 |
0 |
763 |
up |
| GO_NCRNA_PROCESSING |
0.0020121 |
0.0101779 |
0.5697821 |
2.924319 |
0 |
325 |
up |
| GO_RNA_BINDING |
0.0018215 |
0.0101779 |
0.5049426 |
2.917848 |
0 |
1578 |
up |
| GO_RNA_PROCESSING |
0.0018762 |
0.0101779 |
0.5186190 |
2.902894 |
0 |
817 |
up |
| GO_RIBOSOME_ASSEMBLY |
0.0020325 |
0.0101779 |
0.7522069 |
2.899366 |
0 |
52 |
up |
| GO_RNA_CATABOLIC_PROCESS |
0.0020243 |
0.0101779 |
0.5520966 |
2.878377 |
0 |
366 |
up |
| GO_NCRNA_METABOLIC_PROCESS |
0.0020040 |
0.0101779 |
0.5451428 |
2.856717 |
0 |
396 |
up |
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='BAP1 low vs high')

kable(fgp)
| PRC2_EED_UP.V1_DN |
0.0019608 |
0.0057851 |
0.6632460 |
3.169888 |
0 |
179 |
up |
| PDGF_ERK_DN.V1_DN |
0.0019608 |
0.0057851 |
0.6401067 |
2.957151 |
0 |
141 |
up |
| MYC_UP.V1_UP |
0.0019920 |
0.0057851 |
0.6054549 |
2.834592 |
0 |
157 |
up |
| CYCLIN_D1_UP.V1_UP |
0.0019881 |
0.0057851 |
0.5709890 |
2.714571 |
0 |
173 |
up |
| CAMP_UP.V1_UP |
0.0019724 |
0.0057851 |
0.5519773 |
2.635868 |
0 |
181 |
up |
| RB_P130_DN.V1_UP |
0.0019569 |
0.0057851 |
0.5636551 |
2.522018 |
0 |
114 |
up |
| CYCLIN_D1_KE_.V1_UP |
0.0019802 |
0.0057851 |
0.5280465 |
2.518532 |
0 |
178 |
up |
| RAPA_EARLY_UP.V1_DN |
0.0019841 |
0.0057851 |
0.5303480 |
2.507278 |
0 |
167 |
up |
| IL15_UP.V1_UP |
0.0020040 |
0.0057851 |
0.5262108 |
2.502848 |
0 |
174 |
up |
| SRC_UP.V1_UP |
0.0019380 |
0.0057851 |
0.5332113 |
2.480464 |
0 |
148 |
up |
| E2F1_UP.V1_UP |
0.0019881 |
0.0057851 |
0.5208068 |
2.475997 |
0 |
173 |
up |
| ATF2_UP.V1_UP |
0.0019881 |
0.0057851 |
0.5151452 |
2.429911 |
0 |
165 |
up |
| ESC_J1_UP_EARLY.V1_DN |
0.0019960 |
0.0057851 |
0.5213551 |
2.422574 |
0 |
153 |
up |
| RB_DN.V1_UP |
0.0019011 |
0.0057851 |
0.5254773 |
2.389480 |
0 |
123 |
up |
| PIGF_UP.V1_DN |
0.0019724 |
0.0057851 |
0.5008974 |
2.380663 |
0 |
169 |
up |
| RB_P107_DN.V1_UP |
0.0019268 |
0.0057851 |
0.5214990 |
2.376944 |
0 |
128 |
up |
| SIRNA_EIF4GI_UP |
0.0019920 |
0.0057851 |
0.5477723 |
2.345644 |
0 |
87 |
up |
| RPS14_DN.V1_DN |
0.0019841 |
0.0057851 |
0.4911143 |
2.335902 |
0 |
172 |
up |
| IL2_UP.V1_UP |
0.0019802 |
0.0057851 |
0.4751610 |
2.255889 |
0 |
170 |
up |
| CSR_LATE_UP.V1_UP |
0.0019763 |
0.0057851 |
0.4796270 |
2.243683 |
0 |
156 |
up |
| GCNP_SHH_UP_LATE.V1_DN |
0.0019841 |
0.0057851 |
0.4743939 |
2.242749 |
0 |
167 |
up |
| ESC_V6.5_UP_EARLY.V1_UP |
0.0019960 |
0.0057851 |
0.4804199 |
2.229788 |
0 |
152 |
up |
| ESC_V6.5_UP_LATE.V1_DN |
0.0019881 |
0.0057851 |
0.4684776 |
2.209783 |
0 |
165 |
up |
| MEL18_DN.V1_UP |
0.0019417 |
0.0057851 |
0.4837492 |
2.201524 |
0 |
129 |
up |
| ESC_J1_UP_LATE.V1_DN |
0.0020040 |
0.0057851 |
0.4613903 |
2.194538 |
0 |
174 |
up |
| CSR_EARLY_UP.V1_UP |
0.0019455 |
0.0057851 |
0.4704720 |
2.165972 |
0 |
139 |
up |
| BCAT_BILD_ET_AL_UP |
0.0019960 |
0.0057851 |
0.5827447 |
2.155810 |
0 |
43 |
up |
| CRX_NRL_DN.V1_UP |
0.0019011 |
0.0057851 |
0.4696732 |
2.135724 |
0 |
123 |
up |
| AKT_UP_MTOR_DN.V1_UP |
0.0020040 |
0.0057851 |
0.4472208 |
2.109560 |
0 |
166 |
up |
| RAPA_EARLY_UP.V1_UP |
0.0019048 |
0.0057851 |
0.4518858 |
2.105253 |
0 |
146 |
up |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='BAP1 low vs high')

kable(fgp)
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0018939 |
0.0027001 |
0.8136341 |
3.968296 |
0 |
187 |
up |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0019084 |
0.0027001 |
0.7489666 |
3.647362 |
0 |
181 |
up |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN |
0.0018553 |
0.0027001 |
0.7370112 |
3.608971 |
0 |
183 |
up |
| GSE45837_WT_VS_GFI1_KO_PDC_DN |
0.0019194 |
0.0027001 |
0.7381046 |
3.594444 |
0 |
180 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN |
0.0018939 |
0.0027001 |
0.7339672 |
3.579741 |
0 |
187 |
up |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP |
0.0019268 |
0.0027001 |
0.7267557 |
3.484145 |
0 |
162 |
up |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN |
0.0018553 |
0.0027001 |
0.7009428 |
3.432352 |
0 |
183 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0018975 |
0.0027001 |
0.7022270 |
3.429686 |
0 |
191 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0019011 |
0.0027001 |
0.6977299 |
3.403930 |
0 |
189 |
up |
| GSE38681_WT_VS_LYL1_KO_LYMPHOID_PRIMED_MULTIPOTENT_PROGENITOR_UP |
0.0019120 |
0.0027001 |
0.6856263 |
3.336476 |
0 |
179 |
up |
| GSE42724_NAIVE_VS_B1_BCELL_DN |
0.0019231 |
0.0027001 |
0.6795766 |
3.297390 |
0 |
178 |
up |
| GSE42021_CD24LO_TREG_VS_CD24LO_TCONV_THYMUS_DN |
0.0019048 |
0.0027001 |
0.6754033 |
3.295617 |
0 |
185 |
up |
| GSE22589_HEALTHY_VS_SIV_INFECTED_DC_UP |
0.0019120 |
0.0027001 |
0.6695782 |
3.258381 |
0 |
179 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_DN |
0.0018975 |
0.0027001 |
0.6667556 |
3.256443 |
0 |
191 |
up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_DN |
0.0019120 |
0.0027001 |
0.6664943 |
3.251515 |
0 |
193 |
up |
| GSE3337_CTRL_VS_16H_IFNG_IN_CD8POS_DC_DN |
0.0019194 |
0.0027001 |
0.6661061 |
3.243824 |
0 |
180 |
up |
| GSE6269_FLU_VS_E_COLI_INF_PBMC_UP |
0.0019417 |
0.0027001 |
0.6823938 |
3.229015 |
0 |
153 |
up |
| GSE43863_NAIVE_VS_LY6C_LOW_CXCR5NEG_CD4_EFF_TCELL_D6_LCMV_DN |
0.0019380 |
0.0027001 |
0.6680005 |
3.226660 |
0 |
173 |
up |
| GSE42021_CD24HI_TREG_VS_CD24HI_TCONV_THYMUS_UP |
0.0018553 |
0.0027001 |
0.6583079 |
3.223580 |
0 |
183 |
up |
| GSE37532_VISCERAL_ADIPOSE_TISSUE_VS_LN_DERIVED_PPARG_KO_TREG_CD4_TCELL_DN |
0.0019048 |
0.0027001 |
0.6917367 |
3.213316 |
0 |
128 |
up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_UP |
0.0019194 |
0.0027001 |
0.6586656 |
3.212405 |
0 |
194 |
up |
| GSE23568_CTRL_VS_ID3_TRANSDUCED_CD8_TCELL_UP |
0.0018939 |
0.0027001 |
0.6586150 |
3.212229 |
0 |
187 |
up |
| GSE22886_TCELL_VS_BCELL_NAIVE_UP |
0.0019011 |
0.0027001 |
0.6582875 |
3.211507 |
0 |
189 |
up |
| GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN |
0.0018622 |
0.0027001 |
0.6515805 |
3.193919 |
0 |
184 |
up |
| GSE21546_UNSTIM_VS_ANTI_CD3_STIM_DP_THYMOCYTES_DN |
0.0018553 |
0.0027001 |
0.6495656 |
3.180770 |
0 |
183 |
up |
| GSE21670_UNTREATED_VS_IL6_TREATED_CD4_TCELL_UP |
0.0019120 |
0.0027001 |
0.6513792 |
3.169819 |
0 |
179 |
up |
| GSE360_L_DONOVANI_VS_T_GONDII_MAC_DN |
0.0019048 |
0.0027001 |
0.6490942 |
3.164098 |
0 |
188 |
up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0019048 |
0.0027001 |
0.6487939 |
3.163330 |
0 |
190 |
up |
| GSE24634_TREG_VS_TCONV_POST_DAY3_IL4_CONVERSION_UP |
0.0018832 |
0.0027001 |
0.6459728 |
3.160821 |
0 |
182 |
up |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0019048 |
0.0027001 |
0.6477552 |
3.158266 |
0 |
190 |
up |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='BAP1 low vs high')

kable(fgp)
| chr19p13 |
0.0018416 |
0.0064626 |
0.7507847 |
4.070163 |
0 |
544 |
up |
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0019493 |
0.0064626 |
0.8136341 |
3.906648 |
0 |
187 |
up |
| GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN |
0.0019011 |
0.0064626 |
0.7426209 |
3.781248 |
0 |
308 |
up |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0019417 |
0.0064626 |
0.7489666 |
3.585050 |
0 |
181 |
up |
| chr9q34 |
0.0019646 |
0.0064626 |
0.7295889 |
3.541764 |
0 |
210 |
up |
| GSE45837_WT_VS_GFI1_KO_PDC_DN |
0.0019455 |
0.0064626 |
0.7381046 |
3.536428 |
0 |
180 |
up |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN |
0.0019380 |
0.0064626 |
0.7370112 |
3.535072 |
0 |
183 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN |
0.0019493 |
0.0064626 |
0.7339672 |
3.524129 |
0 |
187 |
up |
| MORF_UBE2I |
0.0019194 |
0.0064626 |
0.7133588 |
3.492641 |
0 |
219 |
up |
| MORF_PHB |
0.0020080 |
0.0064626 |
0.7680946 |
3.447925 |
0 |
113 |
up |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP |
0.0019646 |
0.0064626 |
0.7267557 |
3.435344 |
0 |
162 |
up |
| SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP |
0.0018939 |
0.0064626 |
0.6407552 |
3.421352 |
0 |
444 |
up |
| MORF_NME2 |
0.0019380 |
0.0064626 |
0.7289640 |
3.405198 |
0 |
141 |
up |
| LU_EZH2_TARGETS_UP |
0.0019841 |
0.0064626 |
0.6838918 |
3.397405 |
0 |
257 |
up |
| RICKMAN_METASTASIS_DN |
0.0019493 |
0.0064626 |
0.6842922 |
3.394247 |
0 |
246 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0019646 |
0.0064626 |
0.7022270 |
3.375732 |
0 |
191 |
up |
| GO_VIRAL_GENE_EXPRESSION |
0.0019531 |
0.0064626 |
0.7022003 |
3.368209 |
0 |
185 |
up |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN |
0.0019380 |
0.0064626 |
0.7009428 |
3.362070 |
0 |
183 |
up |
| MORF_NPM1 |
0.0019763 |
0.0064626 |
0.7185991 |
3.354154 |
0 |
149 |
up |
| MARTENS_TRETINOIN_RESPONSE_DN |
0.0018149 |
0.0064626 |
0.6052181 |
3.353928 |
0 |
722 |
up |
| MORF_ANP32B |
0.0019380 |
0.0064626 |
0.6985141 |
3.350421 |
0 |
183 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0019724 |
0.0064626 |
0.6977299 |
3.348345 |
0 |
189 |
up |
| MARTENS_BOUND_BY_PML_RARA_FUSION |
0.0019342 |
0.0064626 |
0.6332474 |
3.346672 |
0 |
418 |
up |
| MORF_CSNK2B |
0.0019417 |
0.0064626 |
0.6701245 |
3.342085 |
0 |
258 |
up |
| MORF_ACTG1 |
0.0020325 |
0.0064626 |
0.7308713 |
3.335667 |
0 |
127 |
up |
| MORF_AATF |
0.0019646 |
0.0064626 |
0.6924533 |
3.328748 |
0 |
191 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION |
0.0020284 |
0.0064626 |
0.7426040 |
3.327944 |
0 |
112 |
up |
| MORF_AP2M1 |
0.0019194 |
0.0064626 |
0.6851841 |
3.321971 |
0 |
203 |
up |
| WELCSH_BRCA1_TARGETS_DN |
0.0020325 |
0.0064626 |
0.7266808 |
3.316542 |
0 |
127 |
up |
| MORF_FBL |
0.0020325 |
0.0064626 |
0.7240208 |
3.313485 |
0 |
129 |
up |